MicroManager and Arduino for microscope control

Micro-Manager at the 2008 ASCB annual Meeting in San Francisco

From: http://www.micro-manager.org/case.php?object=ASCB_2008

For the third year in a row, we presented the Micro-Manager software in a booth in the Exhibit Hall at the annual meeting of the ASCB in San Francisco. Our goal was to introduce the Micro-Manager software to people who are not yet aware of its existence, to get feedback from existing Micro-Manager users, and to demonstrate new capabilities for very fast image acquisition.

Drosophile S2 cell expressing GFP-histone and cherry-tubulin (from Eric Griffis). Images were taken during the ASCB meeting at 20 second intervals. At each time point, a z-stack of 5 slices (with 2 micron intervals) was acquired. Exposure time was 66.6 msec, total time to acquire a single time point (10 images) was less than 700 msec. Shown here is a maxmimum intensity projection at each time point.

To demonstrate fast image acquistion we used a spinning disk confocal system (Yokogawa/Solamere) equipped with a Hamamatsu EM camera (C9100-13)ASI XY and piezo X-stage, Zeiss AxioObserver Z1, multi-color laser launch and AOTF (Solamere), Mac Pro computer and screen (Apple) and an Arduino micro-controller. All equipment (except for the Arduino;) was made available to us by the respective company (Thanks!). For fast image acquistion, the camera was run in self-triggered mode, resulting in continuous acquisition at a rate limited almost only by the exposure time. Synchronization of the AOTF and piezo stage can not be accomplished by the computer since the computer has no way of figuring out when exactly the exposure happens. The solution is to use a TTL from the camera that signals when the camera is exposing (many, but not all scientific grade cameras have this capability) and use this TTL to drive a sequence of different output patterns on the Arduino micro-controller. Thus, the TTL of the camera is connected to an input port of the micro-controller. The micro-controller is then instructed to cycle through a sequence of digital output patterns. To this end, we wrote a program that runs on the Arduino and a Micro-Manager device adapter that interacts with this program (available in Micro-Manager version 1.3). A few other useful modes are included in this Arduino program, including a simple/cheap way to control TTLs (6 at the moment, but this can be expanded to 12), ability to do 'blanking' (only expose with light when the camera is exposing), and to run a sequence of events using the build-in clock of the Arduino. We also added a 2-channel DA chip so that we could control light intensity of the AOTF. Acquisition in Micro-Manager is run from a Beanshell script that puts the incoming images in the correct order in the Image5D viewer

 

We were very encouraged by the interest and overwhelmingly positive response both from the user community and from the industry. On the ASCB exhibit floor we noted Micro-Manager controlling equipments in the booths of Point SourceAgilent, and Apogee! Thanks everyone for stopping by at our booth and for all the support our project is getting from the industry!


S2 cells expressing GFP-lamin and cherry-tubulin (from Eric Griffis). Images were taken during the ASCB meeting at 10 second intervals. At each time point, a z-stack of 5 slices (with 1 micron intervals) was acquired. Exposure time was 99.9 msec, total time to acquire a single time point (10 images) was about 1 second. Shown here is a maxmimum intensity projection at each time point.